E.U. Hoped Balkan Border Deal Would Be Model for Peace. Then It Collapsed.

This was supposed to be the year in which Slovenia and Croatia, members of the European Union and NATO, triumphantly ended a 26-year border dispute after an international court ruling in June. But it was not to be.

Slovenia backed the deal, but Croatia had already dropped out of arbitration, accusing Slovenia of breaching the process. The court gave the two countries six months to review the decision and prepare to carry it out.

The deadline expired on Friday.

The collapse of the agreement has left the European Union rattled and more than a little concerned, since it had aimed to use it as a model of amicable conflict resolution for the rest of the Western Balkan countries seeking to join.

Brussels, which had a tense 2017 because of the negotiations over Britain’s exit from the bloc, may be in for a far more difficult 2018, with long-running border disputes on the continent’s volatile southeastern flank.

Here is a look at the Slovenia-Croatia dispute and what’s at stake for the region, and the European Union.

The border row is rooted in the breakup of Yugoslavia in 1991. That year, Slovenia and Croatia were the first of the former Yugoslav republics to declare independence as the others became engulfed in war.

In 1992, the Arbitration Commission of the Peace Conference on Yugoslavia decided that the unmarked boundaries among the newly formed states — Bosnia and Herzegovina, Croatia, Macedonia, Montenegro, Serbia and Slovenia — should become their international borders.

Slovenia and Croatia tried to formalize their maritime and land boundaries in bilateral talks, but could not agree where each country began and ended. After Slovenia joined the European Union in 2004, it blocked Croatia’s accession for years because it would not compromise on the borders.

In 2009, Slovenia lifted the blockade after Croatia agreed to let an arbitration court decide the dispute. That paved the way for Croatia to become a member of the bloc in 2013.

At the center of the dispute are 7.3 square miles of maritime territory in the Bay of Piran in the northern Adriatic Sea. Croatia claims half of the bay.

Also disputed is a 416-mile stretch of land along the Slovene-Croatian border that forms the southern frontier of Europe’s Schengen area, where passport-free travel is possible. Croatia is not member of the Schengen Treaty. But Slovenia, which is, erected a razor-wire fence along that border in 2015 to stem the flow of migrants.

A tribunal in The Hague issued a unanimous decision on June 29, awarding most of the contested waters in the bay to Slovenia. Most crucially, it granted the Alpine country of two million people direct access to international waters via a 10-nautical-mile corridor.

Croatia was awarded contested areas along three rivers in the southeast — Dragonja, Kupa and Mura — as well as territory on a mountain peak called Sveta Gera in Croatia and Trdinov Vrh in Slovenia. The tribunal’s judgment was final, and there is no appeal.

After the ruling, Frans Timmermans, a senior vice president of the European Commission, the European Union’s administrative arm, said, “The commission takes good note of the final award and expects both parties to implement it.”

Slovenia accepted the ruling, but Croatia refused. In 2015, the Zagreb government withdrew from arbitration, citing irreversible damage to the process after an intercepted phone conversation between a lawyer for the Slovene government and an arbiter at the tribunal discussing the case was leaked to the news media.

Slovenia acknowledged the violation, and the Court of Arbitration ruled in 2016 that the leaked call was not enough to force the tribunal to abandon its deliberations.

Since the June ruling, Prime Minister Miro Cerar of Slovenia and Prime Minister Andrej Plenkovic of Croatia have met nine times, with Croatia refusing to change its mind. At their last meeting, in Zagreb on Dec. 19, Mr. Plenkovic reiterated that though the court decision was not binding for his government, it was willing to resolve border issues with its northern neighbor in bilateral talks.

The feud underlines the persistent, deep mistrust among the countries on the edge of the European Union stemming from the wars of the 1990s.

“The European Union underestimated the heavy burden of the past attached to this border dispute and all others in the region,” said Klemen Groselj, a security analyst in Slovenia. “History and current political reality within these countries can defy geography.”

The dispute worries European officials, who are trying to maintain a fragile peace in the Balkans. The European Union had hoped the scarred region had been wrested from the grasp of militant nationalism via funds for reconstruction and a prospect of European integration after democratic reforms.

But the Slovenia-Croatia row is a sign that the nations may be unable to shed troublesome habits, including unending quarrels and threats of unrest.

European officials had considered the new year an important marker to restart its expansion to the Western Balkan countries that have been stuck in the bloc’s waiting room for much of the past decade. The aspiring candidates include Bosnia and Herzegovina, Kosovo, Macedonia, Montenegro and Serbia, along with Albania.

The European Union is also looking to the Western Balkans to fortify the bloc’s external borders by asserting better control of their own frontiers to manage future migrant flows form the south.

Brussels also wants to re-engage the region to fend off the growing influence of Russia, Turkey and China. But various border disputes continue to simmer in the region.

Croatia vs. Serbia

Croatia has a border dispute with each of its neighbors, except Hungary. The most contentious quarrel is over where its national territory ends and Serbia’s begins along a 201-mile stretch of land near the Danube River.

The two countries fought a war in the 1990s and remain bitter rivals. The central question: Does the border run down the middle of the Danube, as Serbia says, or along an old cadastral route, as Croatia claims?

Serbia has been a front-runner in the Western Balkan race for European integration. But as a full member, Croatia can block or delay Serbia’s accession.

Bosnia and Herzegovina vs. Serbia and Croatia

Before ethnic conflict flared in the 1990s between Serbs and Bosniacs in Bosnia and Herzegovina, and before ethnic Croats turned on Bosniacs, the country’s independence had been recognized with its international borders.

But the country was sliced up to end the war. The Dayton peace accord divided it into two entities: one dominated by Serbs and the other shared by Croats and Bosniacs in a federation that was further divided into 10 cantons.

Croats have been itching to break up from the federation and, like the Serbs, have their own entity, including part of the city of Mostar.

The Bosnian Serbs and the leader of their autonomous region, Milorad Dodik, support the quest. Mr. Dodik has consistently undermined the Bosnian courts and other state institutions in Sarajevo to gain more autonomy for his region.

Separately, Croatia has a dispute with Bosnia in the Adriatic Sea.

Bosnia is far from joining the European Union, and failed to fill out a questionnaire that the bloc uses to assess whether a country meets the requirements for joining.

Serbia vs. Kosovo

Kosovo, too, is far from being integrated into the European Union, given that several member nations do not recognize it as a sovereign state. Serbia, which relinquished control of the predominantly ethnic Albanian province after a NATO bombing campaign 18 years ago, does not recognize Kosovo’s independence.

Several thousand troops, including from the United States, remain in Kosovo and patrol the nation’s borders. The Serbian government in Belgrade, meanwhile, has rekindled an old alliance with Russia.

While an armed confrontation between Russia and NATO in the Balkans is unlikely, Moscow supports Belgrade’s refusal to recognize Kosovo’s sovereignty, which it declared in 2008. But without it, Serbia cannot join the European Union.

Kosovo vs. Montenegro

The two countries struck a deal on borders in 2015, but the Kosovo opposition threw a fit — and tear gas in 2016 — in the Parliament chamber, refusing to ratify it because the country had ceded territory.

The European Union, however, set the border demarcation deal with Montenegro as a condition for visa-free travel for Kosovar citizens.

Macedonia vs. Greece

Macedonia is the only former Yugoslav republic to emerge as an independent state without border disputes. But Macedonia’s neighbor, Greece, denies its very existence because it says Macedonia’s name suggests that it has territorial claims over Greece’s own northern region of the same name.

Athens has forced a working name on its neighbor — the Former Yugoslav Republic of Macedonia — and has blocked it from joining any European Union or NATO institution unless it changes its name.